Starting phenix.real_space_refine on Sun Apr 7 01:39:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bss_30165/04_2024/7bss_30165_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 45 5.16 5 C 6043 2.51 5 N 1505 2.21 5 O 1690 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A TYR 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9289 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6604 Classifications: {'peptide': 816} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 793} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.50, per 1000 atoms: 0.59 Number of scatterers: 9289 At special positions: 0 Unit cell: (113.71, 83, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 45 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1690 8.00 N 1505 7.00 C 6043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 401 " - " NAG C 402 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.9 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 37.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.543A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.789A pdb=" N PHE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 118 removed outlier: 5.466A pdb=" N LEU A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 3.908A pdb=" N PHE A 97 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 99 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 100 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 101 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 102 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS A 105 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 107 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 109 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 114 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 116 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 118 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 288 through 315 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.646A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.088A pdb=" N TYR A 360 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 363 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 364 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 366 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 367 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 368 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 679 through 688 removed outlier: 4.315A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.574A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 removed outlier: 4.137A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 802 Processing helix chain 'A' and resid 819 through 826 removed outlier: 4.224A pdb=" N SER A 822 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 823 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 844 No H-bonds generated for 'chain 'A' and resid 841 through 844' Processing helix chain 'A' and resid 853 through 859 removed outlier: 4.014A pdb=" N LYS A 857 " --> pdb=" O HIS A 854 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 894 removed outlier: 3.526A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 3.571A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 908 No H-bonds generated for 'chain 'A' and resid 905 through 908' Processing helix chain 'A' and resid 910 through 913 No H-bonds generated for 'chain 'A' and resid 910 through 913' Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 932 through 936 removed outlier: 3.879A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 936' Processing helix chain 'A' and resid 942 through 945 removed outlier: 3.531A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 974 removed outlier: 3.543A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 removed outlier: 4.006A pdb=" N ILE A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1039 removed outlier: 3.772A pdb=" N ALA A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1064 through 1077 Processing helix chain 'A' and resid 1079 through 1089 removed outlier: 3.654A pdb=" N LEU A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.518A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 333 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.678A pdb=" N ASN C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 133 through 137 removed outlier: 11.736A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 Processing sheet with id= C, first strand: chain 'A' and resid 847 through 849 removed outlier: 3.518A pdb=" N TYR A 847 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 784 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP A 752 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.729A pdb=" N ILE C 311 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 104 through 106 234 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2807 1.33 - 1.46: 1992 1.46 - 1.58: 4649 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 9519 Sorted by residual: bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.795 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.794 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.789 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C3 NAG C 401 " pdb=" O3 NAG C 401 " ideal model delta sigma weight residual 1.403 1.438 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 9514 not shown) Histogram of bond angle deviations from ideal: 89.55 - 107.51: 344 107.51 - 125.47: 12419 125.47 - 143.44: 154 143.44 - 161.40: 0 161.40 - 179.36: 2 Bond angle restraints: 12919 Sorted by residual: angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 178.13 -69.45 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 89.55 20.66 3.00e+00 1.11e-01 4.74e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 89.86 19.83 3.00e+00 1.11e-01 4.37e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.89 19.13 3.00e+00 1.11e-01 4.06e+01 ... (remaining 12914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 5134 22.34 - 44.69: 465 44.69 - 67.03: 61 67.03 - 89.37: 22 89.37 - 111.72: 5 Dihedral angle restraints: 5687 sinusoidal: 2341 harmonic: 3346 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual -86.00 -24.59 -61.41 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA TRP A1045 " pdb=" C TRP A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual -180.00 -152.87 -27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PHE A 894 " pdb=" C PHE A 894 " pdb=" N CYS A 895 " pdb=" CA CYS A 895 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 5684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 1462 0.356 - 0.711: 1 0.711 - 1.067: 0 1.067 - 1.422: 0 1.422 - 1.778: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -0.62 -1.78 2.00e-02 2.50e+03 7.90e+03 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 180 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1461 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG C 405 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.323 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C7 NAG C 404 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.486 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.108 2.00e-02 2.50e+03 9.13e-02 1.04e+02 pdb=" C7 NAG C 402 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.145 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.087 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 74 2.46 - 3.07: 6483 3.07 - 3.68: 13700 3.68 - 4.29: 21653 4.29 - 4.90: 36030 Nonbonded interactions: 77940 Sorted by model distance: nonbonded pdb=" F2 ALF A1101 " pdb="MG MG A1102 " model vdw 1.849 2.120 nonbonded pdb=" O3 NAG C 401 " pdb=" O5 NAG C 402 " model vdw 1.914 2.440 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1102 " model vdw 1.943 2.170 nonbonded pdb=" O THR A 411 " pdb="MG MG A1102 " model vdw 2.082 2.170 nonbonded pdb=" OG SER A 163 " pdb=" O THR A 193 " model vdw 2.111 2.440 ... (remaining 77935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.110 9519 Z= 0.669 Angle : 1.234 69.732 12919 Z= 0.535 Chirality : 0.069 1.778 1464 Planarity : 0.011 0.285 1611 Dihedral : 17.071 111.717 3520 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.60 % Allowed : 18.66 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.18), residues: 1130 helix: -4.49 (0.10), residues: 486 sheet: -3.01 (0.37), residues: 164 loop : -3.22 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.016 0.002 PHE C 214 TYR 0.022 0.002 TYR C 297 ARG 0.003 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 119 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7369 (tt) REVERT: A 330 LYS cc_start: 0.8577 (tmtt) cc_final: 0.7967 (ttmt) REVERT: A 355 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 385 ILE cc_start: 0.8806 (mt) cc_final: 0.8548 (mt) REVERT: A 1055 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8313 (m-80) outliers start: 57 outliers final: 40 residues processed: 171 average time/residue: 0.2578 time to fit residues: 61.4079 Evaluate side-chains 150 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 929 HIS Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 59 ASN A 63 GLN A 106 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 392 ASN A 397 ASN A 862 HIS A 864 HIS A 881 ASN A 888 GLN C 152 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9519 Z= 0.176 Angle : 0.848 29.871 12919 Z= 0.364 Chirality : 0.044 0.358 1464 Planarity : 0.004 0.035 1611 Dihedral : 10.756 82.396 1403 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.72 % Allowed : 20.83 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.21), residues: 1130 helix: -2.90 (0.17), residues: 492 sheet: -2.59 (0.37), residues: 167 loop : -2.59 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.015 0.001 PHE A 894 TYR 0.012 0.001 TYR A 324 ARG 0.002 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7224 (p0) cc_final: 0.6969 (p0) REVERT: A 272 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 330 LYS cc_start: 0.8580 (tmtt) cc_final: 0.7950 (ttmt) REVERT: A 760 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8039 (mp) REVERT: C 146 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: C 152 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7948 (p0) REVERT: C 184 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8018 (mt-10) REVERT: C 305 ASP cc_start: 0.8207 (t0) cc_final: 0.7833 (t0) outliers start: 48 outliers final: 22 residues processed: 167 average time/residue: 0.2274 time to fit residues: 53.3231 Evaluate side-chains 137 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9519 Z= 0.178 Angle : 0.831 29.909 12919 Z= 0.352 Chirality : 0.045 0.402 1464 Planarity : 0.004 0.036 1611 Dihedral : 8.303 59.279 1361 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.13 % Allowed : 21.22 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.23), residues: 1130 helix: -1.97 (0.20), residues: 485 sheet: -2.04 (0.42), residues: 145 loop : -2.27 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 PHE 0.016 0.001 PHE A1032 TYR 0.013 0.001 TYR A 324 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.082 Fit side-chains REVERT: A 121 ASN cc_start: 0.7026 (p0) cc_final: 0.6788 (p0) REVERT: A 272 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 330 LYS cc_start: 0.8529 (tmtt) cc_final: 0.7860 (ttmt) REVERT: A 355 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 940 ARG cc_start: 0.7189 (ptt-90) cc_final: 0.6847 (ptt-90) REVERT: C 305 ASP cc_start: 0.8212 (t0) cc_final: 0.7832 (t0) outliers start: 42 outliers final: 25 residues processed: 159 average time/residue: 0.2129 time to fit residues: 47.5717 Evaluate side-chains 142 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 279 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0970 chunk 77 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9519 Z= 0.132 Angle : 0.797 29.827 12919 Z= 0.333 Chirality : 0.043 0.395 1464 Planarity : 0.003 0.035 1611 Dihedral : 6.605 59.406 1354 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.05 % Allowed : 22.20 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1130 helix: -1.37 (0.22), residues: 490 sheet: -1.52 (0.44), residues: 141 loop : -2.21 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.012 0.001 PHE A1032 TYR 0.012 0.001 TYR A 324 ARG 0.008 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.076 Fit side-chains REVERT: A 121 ASN cc_start: 0.6602 (p0) cc_final: 0.6198 (p0) REVERT: A 272 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7620 (tt) REVERT: A 330 LYS cc_start: 0.8449 (tmtt) cc_final: 0.7797 (ttmt) REVERT: A 355 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8559 (mp) REVERT: A 364 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7881 (pp20) REVERT: C 305 ASP cc_start: 0.8202 (t0) cc_final: 0.7887 (t0) outliers start: 31 outliers final: 18 residues processed: 151 average time/residue: 0.2141 time to fit residues: 45.5107 Evaluate side-chains 138 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 279 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 9519 Z= 0.590 Angle : 0.951 31.086 12919 Z= 0.423 Chirality : 0.052 0.419 1464 Planarity : 0.005 0.043 1611 Dihedral : 7.236 58.469 1347 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.30 % Allowed : 21.61 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1130 helix: -1.80 (0.20), residues: 502 sheet: -1.31 (0.45), residues: 143 loop : -2.28 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.022 0.002 PHE A 995 TYR 0.025 0.002 TYR C 297 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 1.055 Fit side-chains REVERT: A 121 ASN cc_start: 0.7693 (p0) cc_final: 0.7465 (p0) REVERT: A 126 TYR cc_start: 0.7903 (m-80) cc_final: 0.7539 (m-10) REVERT: A 272 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7553 (tt) REVERT: A 330 LYS cc_start: 0.8585 (tmtt) cc_final: 0.7915 (ttmt) REVERT: A 355 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 364 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7952 (pp20) REVERT: A 714 ARG cc_start: 0.5940 (mmm160) cc_final: 0.5576 (mmm160) REVERT: C 152 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7996 (p0) REVERT: C 305 ASP cc_start: 0.8273 (t0) cc_final: 0.7906 (t0) outliers start: 54 outliers final: 39 residues processed: 154 average time/residue: 0.2193 time to fit residues: 47.8796 Evaluate side-chains 144 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 101 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9519 Z= 0.194 Angle : 0.814 29.865 12919 Z= 0.346 Chirality : 0.044 0.408 1464 Planarity : 0.004 0.034 1611 Dihedral : 6.541 59.137 1347 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.03 % Allowed : 22.99 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1130 helix: -1.22 (0.22), residues: 484 sheet: -1.35 (0.44), residues: 146 loop : -1.97 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 323 HIS 0.010 0.001 HIS C 302 PHE 0.015 0.001 PHE A 894 TYR 0.014 0.001 TYR A 324 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.063 Fit side-chains REVERT: A 272 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 330 LYS cc_start: 0.8486 (tmtt) cc_final: 0.7818 (ttmt) REVERT: A 355 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 364 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: C 152 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7938 (p0) REVERT: C 305 ASP cc_start: 0.8217 (t0) cc_final: 0.7824 (t0) outliers start: 41 outliers final: 31 residues processed: 145 average time/residue: 0.2129 time to fit residues: 43.9709 Evaluate side-chains 140 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9519 Z= 0.213 Angle : 0.814 30.159 12919 Z= 0.344 Chirality : 0.044 0.399 1464 Planarity : 0.003 0.034 1611 Dihedral : 6.299 59.886 1347 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.72 % Allowed : 22.99 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.25), residues: 1130 helix: -0.94 (0.23), residues: 484 sheet: -1.30 (0.44), residues: 150 loop : -1.84 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.013 0.001 PHE A 971 TYR 0.014 0.001 TYR A 324 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 108 time to evaluate : 1.106 Fit side-chains REVERT: A 266 MET cc_start: 0.7894 (mmt) cc_final: 0.7598 (mmp) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 330 LYS cc_start: 0.8503 (tmtt) cc_final: 0.7830 (ttmt) REVERT: A 355 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 364 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: A 979 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7468 (mm-40) REVERT: C 152 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7901 (p0) REVERT: C 305 ASP cc_start: 0.8204 (t0) cc_final: 0.7862 (t0) outliers start: 48 outliers final: 36 residues processed: 148 average time/residue: 0.2056 time to fit residues: 43.4263 Evaluate side-chains 146 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 105 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN C 254 ASN C 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9519 Z= 0.133 Angle : 0.792 29.796 12919 Z= 0.331 Chirality : 0.043 0.383 1464 Planarity : 0.003 0.034 1611 Dihedral : 5.951 59.985 1345 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.13 % Allowed : 24.17 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 1130 helix: -0.70 (0.23), residues: 492 sheet: -0.96 (0.46), residues: 143 loop : -1.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 323 HIS 0.010 0.001 HIS C 302 PHE 0.018 0.001 PHE A1032 TYR 0.016 0.001 TYR A 879 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.137 Fit side-chains REVERT: A 272 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7653 (tt) REVERT: A 330 LYS cc_start: 0.8424 (tmtt) cc_final: 0.7778 (ttmt) REVERT: A 355 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 364 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7915 (pp20) REVERT: A 979 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7360 (mm-40) REVERT: C 152 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 305 ASP cc_start: 0.8185 (t0) cc_final: 0.7843 (t0) outliers start: 42 outliers final: 33 residues processed: 149 average time/residue: 0.2038 time to fit residues: 43.5021 Evaluate side-chains 144 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9519 Z= 0.266 Angle : 0.835 30.317 12919 Z= 0.353 Chirality : 0.045 0.390 1464 Planarity : 0.004 0.041 1611 Dihedral : 6.064 59.441 1345 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.42 % Allowed : 24.26 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.25), residues: 1130 helix: -0.72 (0.23), residues: 486 sheet: -1.08 (0.45), residues: 150 loop : -1.69 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.006 0.001 HIS C 302 PHE 0.017 0.001 PHE A1032 TYR 0.016 0.001 TYR A 324 ARG 0.007 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 1.032 Fit side-chains REVERT: A 272 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7619 (tt) REVERT: A 330 LYS cc_start: 0.8474 (tmtt) cc_final: 0.7821 (ttmt) REVERT: A 355 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 364 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8191 (pp20) REVERT: A 979 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: A 1053 MET cc_start: 0.7933 (ptp) cc_final: 0.7538 (mtt) REVERT: C 152 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7907 (p0) REVERT: C 305 ASP cc_start: 0.8204 (t0) cc_final: 0.7789 (t0) outliers start: 45 outliers final: 34 residues processed: 145 average time/residue: 0.1988 time to fit residues: 40.9686 Evaluate side-chains 141 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 102 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9519 Z= 0.215 Angle : 0.825 30.160 12919 Z= 0.347 Chirality : 0.045 0.390 1464 Planarity : 0.004 0.038 1611 Dihedral : 6.031 59.483 1345 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.03 % Allowed : 24.75 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1130 helix: -0.59 (0.24), residues: 481 sheet: -0.98 (0.45), residues: 150 loop : -1.64 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 PHE 0.014 0.001 PHE A1032 TYR 0.017 0.001 TYR A 879 ARG 0.007 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.095 Fit side-chains REVERT: A 272 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7645 (tt) REVERT: A 330 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7791 (ttmt) REVERT: A 355 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 364 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: A 926 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 979 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7397 (mm-40) REVERT: C 152 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7897 (p0) REVERT: C 305 ASP cc_start: 0.8205 (t0) cc_final: 0.7753 (t0) outliers start: 41 outliers final: 33 residues processed: 144 average time/residue: 0.2104 time to fit residues: 43.1552 Evaluate side-chains 146 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 0.0050 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115505 restraints weight = 11385.716| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.83 r_work: 0.2951 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9519 Z= 0.178 Angle : 0.807 30.044 12919 Z= 0.338 Chirality : 0.044 0.385 1464 Planarity : 0.003 0.036 1611 Dihedral : 5.893 59.726 1345 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.73 % Allowed : 25.64 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.25), residues: 1130 helix: -0.46 (0.24), residues: 483 sheet: -0.89 (0.45), residues: 150 loop : -1.65 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.012 0.001 PHE A 971 TYR 0.017 0.001 TYR A 879 ARG 0.007 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.45 seconds wall clock time: 42 minutes 42.50 seconds (2562.50 seconds total)